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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in CTR_kf284_0002.multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 0.9.dev0

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Project ID ::: CTR_kf284_0002
        Centre for Trophoblast Research, University of Cambridge

        Created by CTR Bioinformatics

        Analysis by:
        Russell S. Hamilton
        Contact E-mail:
        rsh46@cam.ac.uk
        Application Type:
        RNA-seq
        Project Type:
        RNA-Seq Quality Control
        Project Owners:
        Damiano Giuseppe Barone / Kristian Franze
        Sequencing Platform:
        Illumina
        Sequencing Setup:
        SE 50bp

        Report generated on 2017-11-22, 15:11 based on data in: /rds/project/rsh46/rds-rsh46-ctr-bfx/CTR-Projects/CTR_kf284_0002


        General Statistics

        Showing 1310 samples.

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        QualiMap

        QualiMap is a platform-independent application to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

        Genomic origin of reads


        Gene Coverage Profile


        STAR

        STAR is an ultrafast universal RNA-seq aligner.


        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.


        FastQ Screen

        FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

        Summed alignment percentages are shown below. Note that percentages can sum to greater than 100% if reads align to multiple organisms.


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Quality Histograms

        The mean quality value across each base position in the read. See the FastQC help.


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

        Click a heatmap row to see a line plot for that dataset.

        rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.


        Per Base N Content

        The percentage of base calls at each position for which an N was called. See the FastQC help.


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help.


        Sequence Duplication Levels

        The relative level of duplication found for every sequence. See the FastQC help.


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.